Spinal cord data
Contents
Spinal cord data#
Spinal cord CSA#
Code imports#
# Python imports
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd
# Import custom tools
from tools.data import Data
from tools.plot import Plot
Download data#
data_type = 'spine'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
--2022-06-14 04:16:51-- https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response...
Archive: spinalcord_results.zip
inflating: data/spine/DWI_RD.csv
inflating: data/spine/DWI_FA.csv
inflating: data/spine/csa-SC_T2w.csv
inflating: data/spine/DWI_MD.csv
inflating: data/spine/MTR.csv
inflating: data/spine/MTsat.csv
inflating: data/spine/csa-GM_T2s.csv
inflating: data/spine/csa-SC_T1w.csv
inflating: data/spine/._csa-SC_T1w.csv
inflating: data/spine/T1.csv
302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T041652Z&X-Amz-Expires=300&X-Amz-Signature=e1a2a87dd141ae63bf2ce9bce563010ddb85ab7a45466dd015e57ab2eb6ee393&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 04:16:52-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T041652Z&X-Amz-Expires=300&X-Amz-Signature=e1a2a87dd141ae63bf2ce9bce563010ddb85ab7a45466dd015e57ab2eb6ee393&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’
0K .......... ........ 100% 13.4M=0.001s
2022-06-14 04:16:52 (13.4 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]
Load data plot it#
dataset.load()
fig_spine = Plot(dataset, plot_name = 'spine-1')
fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'WM')
[[67.68043139343541, 67.51192950187651, 64.10906141748492, -100], [66.45528870474881, 73.68810861718586, 73.90549406140528, 69.40567255226951], [59.92768078307679, 60.228813886890336, 60.62168402306773, 59.91566547643056], [-100, 59.71785704128032, 61.9692210118123, -100], [53.01001344464832, 64.7179719462451, -100, -100], [62.953113761654, 64.82356608772385, 62.99080203229852, 63.92581015491735]]
[[80.31287669419582, 80.7684228622334, 80.77416179502649, -100], [92.72412473358578, 94.58771243953994, 92.66689980123054, 93.57146821082088], [73.61777268131331, 72.98017043131877, 70.59364812603286, 71.2682278628924], [-100, 74.7323749938961, 75.00564528070014, -100], [70.77995321551784, 74.85780653908817, -100, -100], [72.95826654799964, 73.12988138337275, 73.89480466120321, 72.12924398136843]]
[[7.907950710951821, 7.843773703968845, 7.631687563651485, -100], [7.129077482842031, 7.810909329377152, 7.638262398298541, 7.281050825550765], [7.548970304998321, 7.289425820272084, 7.247625600797361, 7.260624668805574], [-100, 6.888135342166283, 7.154947720361157, -100], [6.160486531216797, 7.214461332923804, -100, -100], [6.9764697490594285, 8.490406614178003, 6.948269241835464, 6.947796748890014]]
[[8.588306094862464, 8.582343691515673, 8.59951772651972, -100], [8.778401001405253, 8.850984184640001, 8.678719730381427, 8.82272455460417], [8.049736168344822, 7.97524740913002, 7.964590642340806, 8.037643135115415], [-100, 7.884773416702429, 7.95820728195736, -100], [7.452694732402675, 7.768883514962651, -100, -100], [7.565961173939572, 7.522650763063116, 7.569823513645105, 7.458338068065783]]
[[10.843163978642025, 10.874612368804629, 10.640776068173537, -100], [11.992442659094293, 12.065046487001773, 12.371407759118163, 12.227376084450857], [10.086060382315525, 10.48696693008013, 10.63286922157809, 10.44556244714515], [-100, 10.99912755279636, 10.956738998211137, -100], [10.9652750623018, 11.448593985144951, -100, -100], [11.51311336799651, 9.50311253291029, 11.50666070966459, 11.72760399036461]]
[[11.899994066574813, 11.935064110735278, 11.942164559607434, -100], [13.469830989154392, 13.618790091744144, 13.567127631981656, 13.510144283287582], [11.618506415709447, 11.66900621016246, 11.24624373129029, 11.275181029280414], [-100, 12.063074043369465, 11.967497282819402, -100], [12.19036818126348, 12.4019702605711, -100, -100], [12.298751781746718, 12.384760953392885, 12.44979374309126, 12.327044809492431]]
[[-4.254821566319245, -6.577358093753865, -4.670982803353963, -100], [0.0958291914789581, -0.0683220814153947, -0.6915323825239118, -0.7490075844343679], [-0.7786169618659662, -1.464265417872741, -0.0094776277273878, -2.222570167476504], [-100, 2.572137883831496, 6.989457951802857, -100], [-1.7908240068464327, -3.0346801596491813, -100, -100], [-0.6462460004756462, 13.11346638058934, -2.3383486281915142, -1.1325263581337364]]
[[-3.958454322934591, -5.074402801870328, -3.76006797019974, -100], [-0.5335915782748561, -0.8551573134169094, -0.5962556423462212, -1.3103819488313022], [-0.1765591140429531, -0.1690887168825523, -0.9913636312482512, 0.1498274918613771], [-100, -0.0570756403278655, 4.142685856847653, -100], [-1.899860201989412, -2.745917236367505, -100, -100], [-0.2300002150227979, -0.9599232843254364, 0.5471777663632511, -2.1454139832601533]]
[[67.68043139343541, 67.51192950187651, 64.10906141748492, -100], [66.45528870474881, 73.68810861718586, 73.90549406140528, 69.40567255226951], [59.92768078307679, 60.228813886890336, 60.62168402306773, 59.91566547643056], [-100, 59.71785704128032, 61.9692210118123, -100], [53.01001344464832, 64.7179719462451, -100, -100], [62.953113761654, 64.82356608772385, 62.99080203229852, 63.92581015491735]]
[[80.31287669419582, 80.7684228622334, 80.77416179502649, -100], [92.72412473358578, 94.58771243953994, 92.66689980123054, 93.57146821082088], [73.61777268131331, 72.98017043131877, 70.59364812603286, 71.2682278628924], [-100, 74.7323749938961, 75.00564528070014, -100], [70.77995321551784, 74.85780653908817, -100, -100], [72.95826654799964, 73.12988138337275, 73.89480466120321, 72.12924398136843]]
[[7.907950710951821, 7.843773703968845, 7.631687563651485, -100], [7.129077482842031, 7.810909329377152, 7.638262398298541, 7.281050825550765], [7.548970304998321, 7.289425820272084, 7.247625600797361, 7.260624668805574], [-100, 6.888135342166283, 7.154947720361157, -100], [6.160486531216797, 7.214461332923804, -100, -100], [6.9764697490594285, 8.490406614178003, 6.948269241835464, 6.947796748890014]]
[[8.588306094862464, 8.582343691515673, 8.59951772651972, -100], [8.778401001405253, 8.850984184640001, 8.678719730381427, 8.82272455460417], [8.049736168344822, 7.97524740913002, 7.964590642340806, 8.037643135115415], [-100, 7.884773416702429, 7.95820728195736, -100], [7.452694732402675, 7.768883514962651, -100, -100], [7.565961173939572, 7.522650763063116, 7.569823513645105, 7.458338068065783]]
[[10.843163978642025, 10.874612368804629, 10.640776068173537, -100], [11.992442659094293, 12.065046487001773, 12.371407759118163, 12.227376084450857], [10.086060382315525, 10.48696693008013, 10.63286922157809, 10.44556244714515], [-100, 10.99912755279636, 10.956738998211137, -100], [10.9652750623018, 11.448593985144951, -100, -100], [11.51311336799651, 9.50311253291029, 11.50666070966459, 11.72760399036461]]
[[11.899994066574813, 11.935064110735278, 11.942164559607434, -100], [13.469830989154392, 13.618790091744144, 13.567127631981656, 13.510144283287582], [11.618506415709447, 11.66900621016246, 11.24624373129029, 11.275181029280414], [-100, 12.063074043369465, 11.967497282819402, -100], [12.19036818126348, 12.4019702605711, -100, -100], [12.298751781746718, 12.384760953392885, 12.44979374309126, 12.327044809492431]]
[[-4.254821566319245, -6.577358093753865, -4.670982803353963, -100], [0.0958291914789581, -0.0683220814153947, -0.6915323825239118, -0.7490075844343679], [-0.7786169618659662, -1.464265417872741, -0.0094776277273878, -2.222570167476504], [-100, 2.572137883831496, 6.989457951802857, -100], [-1.7908240068464327, -3.0346801596491813, -100, -100], [-0.6462460004756462, 13.11346638058934, -2.3383486281915142, -1.1325263581337364]]
[[-3.958454322934591, -5.074402801870328, -3.76006797019974, -100], [-0.5335915782748561, -0.8551573134169094, -0.5962556423462212, -1.3103819488313022], [-0.1765591140429531, -0.1690887168825523, -0.9913636312482512, 0.1498274918613771], [-100, -0.0570756403278655, 4.142685856847653, -100], [-1.899860201989412, -2.745917236367505, -100, -100], [-0.2300002150227979, -0.9599232843254364, 0.5471777663632511, -2.1454139832601533]]
[[ 67.68043139 67.5119295 64.10906142 -100. ]
[ 66.4552887 73.68810862 73.90549406 69.40567255]
[ 59.92768078 60.22881389 60.62168402 59.91566548]
[-100. 59.71785704 61.96922101 -100. ]
[ 53.01001344 64.71797195 -100. -100. ]
[ 62.95311376 64.82356609 62.99080203 63.92581015]
[ 80.31287669 80.76842286 80.7741618 -100. ]
[ 92.72412473 94.58771244 92.6668998 93.57146821]
[ 73.61777268 72.98017043 70.59364813 71.26822786]
[-100. 74.73237499 75.00564528 -100. ]
[ 70.77995322 74.85780654 -100. -100. ]
[ 72.95826655 73.12988138 73.89480466 72.12924398]]
[[ 67.68043139 67.5119295 64.10906142 -100. ]
[ 66.4552887 73.68810862 73.90549406 69.40567255]
[ 59.92768078 60.22881389 60.62168402 59.91566548]
[-100. 59.71785704 61.96922101 -100. ]
[ 53.01001344 64.71797195 -100. -100. ]
[ 62.95311376 64.82356609 62.99080203 63.92581015]
[ 80.31287669 80.76842286 80.7741618 -100. ]
[ 92.72412473 94.58771244 92.6668998 93.57146821]
[ 73.61777268 72.98017043 70.59364813 71.26822786]
[-100. 74.73237499 75.00564528 -100. ]
[ 70.77995322 74.85780654 -100. -100. ]
[ 72.95826655 73.12988138 73.89480466 72.12924398]]
[[ 7.90795071 7.8437737 7.63168756 -100. ]
[ 7.12907748 7.81090933 7.6382624 7.28105083]
[ 7.5489703 7.28942582 7.2476256 7.26062467]
[-100. 6.88813534 7.15494772 -100. ]
[ 6.16048653 7.21446133 -100. -100. ]
[ 6.97646975 8.49040661 6.94826924 6.94779675]
[ 8.58830609 8.58234369 8.59951773 -100. ]
[ 8.778401 8.85098418 8.67871973 8.82272455]
[ 8.04973617 7.97524741 7.96459064 8.03764314]
[-100. 7.88477342 7.95820728 -100. ]
[ 7.45269473 7.76888351 -100. -100. ]
[ 7.56596117 7.52265076 7.56982351 7.45833807]]
[[ 7.90795071 7.8437737 7.63168756 -100. ]
[ 7.12907748 7.81090933 7.6382624 7.28105083]
[ 7.5489703 7.28942582 7.2476256 7.26062467]
[-100. 6.88813534 7.15494772 -100. ]
[ 6.16048653 7.21446133 -100. -100. ]
[ 6.97646975 8.49040661 6.94826924 6.94779675]
[ 8.58830609 8.58234369 8.59951773 -100. ]
[ 8.778401 8.85098418 8.67871973 8.82272455]
[ 8.04973617 7.97524741 7.96459064 8.03764314]
[-100. 7.88477342 7.95820728 -100. ]
[ 7.45269473 7.76888351 -100. -100. ]
[ 7.56596117 7.52265076 7.56982351 7.45833807]]
[[ 10.84316398 10.87461237 10.64077607 -100. ]
[ 11.99244266 12.06504649 12.37140776 12.22737608]
[ 10.08606038 10.48696693 10.63286922 10.44556245]
[-100. 10.99912755 10.956739 -100. ]
[ 10.96527506 11.44859399 -100. -100. ]
[ 11.51311337 9.50311253 11.50666071 11.72760399]
[ 11.89999407 11.93506411 11.94216456 -100. ]
[ 13.46983099 13.61879009 13.56712763 13.51014428]
[ 11.61850642 11.66900621 11.24624373 11.27518103]
[-100. 12.06307404 11.96749728 -100. ]
[ 12.19036818 12.40197026 -100. -100. ]
[ 12.29875178 12.38476095 12.44979374 12.32704481]]
[[ 10.84316398 10.87461237 10.64077607 -100. ]
[ 11.99244266 12.06504649 12.37140776 12.22737608]
[ 10.08606038 10.48696693 10.63286922 10.44556245]
[-100. 10.99912755 10.956739 -100. ]
[ 10.96527506 11.44859399 -100. -100. ]
[ 11.51311337 9.50311253 11.50666071 11.72760399]
[ 11.89999407 11.93506411 11.94216456 -100. ]
[ 13.46983099 13.61879009 13.56712763 13.51014428]
[ 11.61850642 11.66900621 11.24624373 11.27518103]
[-100. 12.06307404 11.96749728 -100. ]
[ 12.19036818 12.40197026 -100. -100. ]
[ 12.29875178 12.38476095 12.44979374 12.32704481]]
[[-4.25482157e+00 -6.57735809e+00 -4.67098280e+00 -1.00000000e+02]
[ 9.58291915e-02 -6.83220814e-02 -6.91532383e-01 -7.49007584e-01]
[-7.78616962e-01 -1.46426542e+00 -9.47762773e-03 -2.22257017e+00]
[-1.00000000e+02 2.57213788e+00 6.98945795e+00 -1.00000000e+02]
[-1.79082401e+00 -3.03468016e+00 -1.00000000e+02 -1.00000000e+02]
[-6.46246000e-01 1.31134664e+01 -2.33834863e+00 -1.13252636e+00]
[-3.95845432e+00 -5.07440280e+00 -3.76006797e+00 -1.00000000e+02]
[-5.33591578e-01 -8.55157313e-01 -5.96255642e-01 -1.31038195e+00]
[-1.76559114e-01 -1.69088717e-01 -9.91363631e-01 1.49827492e-01]
[-1.00000000e+02 -5.70756403e-02 4.14268586e+00 -1.00000000e+02]
[-1.89986020e+00 -2.74591724e+00 -1.00000000e+02 -1.00000000e+02]
[-2.30000215e-01 -9.59923284e-01 5.47177766e-01 -2.14541398e+00]]
[[-4.25482157e+00 -6.57735809e+00 -4.67098280e+00 -1.00000000e+02]
[ 9.58291915e-02 -6.83220814e-02 -6.91532383e-01 -7.49007584e-01]
[-7.78616962e-01 -1.46426542e+00 -9.47762773e-03 -2.22257017e+00]
[-1.00000000e+02 2.57213788e+00 6.98945795e+00 -1.00000000e+02]
[-1.79082401e+00 -3.03468016e+00 -1.00000000e+02 -1.00000000e+02]
[-6.46246000e-01 1.31134664e+01 -2.33834863e+00 -1.13252636e+00]
[-3.95845432e+00 -5.07440280e+00 -3.76006797e+00 -1.00000000e+02]
[-5.33591578e-01 -8.55157313e-01 -5.96255642e-01 -1.31038195e+00]
[-1.76559114e-01 -1.69088717e-01 -9.91363631e-01 1.49827492e-01]
[-1.00000000e+02 -5.70756403e-02 4.14268586e+00 -1.00000000e+02]
[-1.89986020e+00 -2.74591724e+00 -1.00000000e+02 -1.00000000e+02]
[-2.30000215e-01 -9.59923284e-01 5.47177766e-01 -2.14541398e+00]]
[[ 67.68043139 67.5119295 64.10906142 -100. ]
[ 66.4552887 73.68810862 73.90549406 69.40567255]
[ 59.92768078 60.22881389 60.62168402 59.91566548]
[-100. 59.71785704 61.96922101 -100. ]
[ 53.01001344 64.71797195 -100. -100. ]
[ 62.95311376 64.82356609 62.99080203 63.92581015]
[ 80.31287669 80.76842286 80.7741618 -100. ]
[ 92.72412473 94.58771244 92.6668998 93.57146821]
[ 73.61777268 72.98017043 70.59364813 71.26822786]
[-100. 74.73237499 75.00564528 -100. ]
[ 70.77995322 74.85780654 -100. -100. ]
[ 72.95826655 73.12988138 73.89480466 72.12924398]]
[[ 67.68043139 67.5119295 64.10906142 -100. ]
[ 66.4552887 73.68810862 73.90549406 69.40567255]
[ 59.92768078 60.22881389 60.62168402 59.91566548]
[-100. 59.71785704 61.96922101 -100. ]
[ 53.01001344 64.71797195 -100. -100. ]
[ 62.95311376 64.82356609 62.99080203 63.92581015]
[ 80.31287669 80.76842286 80.7741618 -100. ]
[ 92.72412473 94.58771244 92.6668998 93.57146821]
[ 73.61777268 72.98017043 70.59364813 71.26822786]
[-100. 74.73237499 75.00564528 -100. ]
[ 70.77995322 74.85780654 -100. -100. ]
[ 72.95826655 73.12988138 73.89480466 72.12924398]]
Gray matter CSA#
fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord gray matter CSA'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'GM')
[[15.781249999999996, 15.928571428571423, 16.999999999999996, -100], [19.821428571428573, 20.0, 19.214285714285705, 20.464285714285705], [18.20833333333333, 17.333333333333325, 16.624999999999996, 16.958333333333325], [-100, 17.041666666666657, 17.333332300186154, -100], [16.214285714285708, -100, -100, -100], [16.64285714285713, 17.392857142857142, 16.32142759859562, 16.53571428571428]]
[[15.781249999999996, 15.928571428571423, 16.999999999999996, -100], [19.821428571428573, 20.0, 19.214285714285705, 20.464285714285705], [18.20833333333333, 17.333333333333325, 16.624999999999996, 16.958333333333325], [-100, 17.041666666666657, 17.333332300186154, -100], [16.214285714285708, -100, -100, -100], [16.64285714285713, 17.392857142857142, 16.32142759859562, 16.53571428571428]]
[[15.781249999999996, 15.928571428571423, 16.999999999999996, -100], [19.821428571428573, 20.0, 19.214285714285705, 20.464285714285705], [18.20833333333333, 17.333333333333325, 16.624999999999996, 16.958333333333325], [-100, 17.041666666666657, 17.333332300186154, -100], [16.214285714285708, -100, -100, -100], [16.64285714285713, 17.392857142857142, 16.32142759859562, 16.53571428571428]]
[[15.781249999999996, 15.928571428571423, 16.999999999999996, -100], [19.821428571428573, 20.0, 19.214285714285705, 20.464285714285705], [18.20833333333333, 17.333333333333325, 16.624999999999996, 16.958333333333325], [-100, 17.041666666666657, 17.333332300186154, -100], [16.214285714285708, -100, -100, -100], [16.64285714285713, 17.392857142857142, 16.32142759859562, 16.53571428571428]]
White matter qMRI#
data_type = 'qmri'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
--2022-06-14 04:16:53-- https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response...
Archive: spinalcord_results.zip
inflating: data/qmri/DWI_RD.csv
inflating: data/qmri/DWI_FA.csv
inflating: data/qmri/csa-SC_T2w.csv
inflating: data/qmri/DWI_MD.csv
inflating: data/qmri/MTR.csv
inflating: data/qmri/MTsat.csv
inflating: data/qmri/csa-GM_T2s.csv
inflating: data/qmri/csa-SC_T1w.csv
inflating: data/qmri/._csa-SC_T1w.csv
inflating: data/qmri/T1.csv
302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T041652Z&X-Amz-Expires=300&X-Amz-Signature=e1a2a87dd141ae63bf2ce9bce563010ddb85ab7a45466dd015e57ab2eb6ee393&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 04:16:53-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T041652Z&X-Amz-Expires=300&X-Amz-Signature=e1a2a87dd141ae63bf2ce9bce563010ddb85ab7a45466dd015e57ab2eb6ee393&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’
0K .......... ........ 100% 16.5M=0.001s
2022-06-14 04:16:53 (16.5 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]
dataset.load()
fig_spine = Plot(dataset, plot_name = 'spine-3')
fig_spine.title = 'Spinal cord qMRI microstructure'
matrix = dataset.extract_data('qmri')
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'WM')
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]
DWI_FA
[[0.0010138856451204, 0.0010177543993774, 0.0010257196398529, 0.0010257196398529], [0.0014014718331852, 0.0009761721717434, 0.0009117604540341, 0.000815311519069], [0.0009605911746559, 0.0009906206359397, 0.0006694445137909, 0.0008935883019168], [0.0008935883019168, 0.0009645148099392, 0.0010351902433702, 0.0010351902433702], [0.0009774778167169, 0.0009774778167169, 0.0009774778167169, 0.0009774778167169], [0.0010551867192628, 0.001012210010244, 0.0010180580331023, 0.0009165329349018]]
DWI_MD
[[0.0005942976466395, 0.0005960152894725, 0.00062691302888, 0.00062691302888], [0.0005112709262059, 0.0005704880839017, 0.0005137069084603, 0.0004143742226968], [0.0004672565333558, 0.0005026007210642, 0.0004066867643462, 0.0003393328073422], [0.0003393328073422, 0.0004692023931709, 0.0005123971557951, 0.0005123971557951], [0.0005045102052002, 0.0005045102052002, 0.0005045102052002, 0.0005045102052002], [0.000577999230138, 0.0005316527869437, 0.0005729917043376, 0.0004937373474434]]
DWI_RD
[[44.209522055240505, 50.69960144846205, 45.682771475180594, 45.682771475180594], [42.67916913302598, 37.82261433907465, 44.258456219263856, 40.76688074907387], [47.497071935829645, 47.81068337186637, 47.57378502229639, 47.19708621549288], [47.19708621549288, 46.77334882206762, 47.79720317144616, 47.79720317144616], [46.802709566692286, 44.27238222794652, 44.27238222794652, 44.27238222794652], [47.15066198433709, 46.34750036374999, 48.02207246120396, 45.055435263858136]]
MTR
[[3.499265814909754, 3.80693641422522, 3.3575814030216278, 3.3575814030216278], [3.8557974910487354, 2.846363452702357, 4.075625383910599, 3.373417235607917], [3.7244854393057487, 3.704874827322425, 3.589619356583784, 3.442284461661099], [3.442284461661099, 3.539465912889603, 3.637115993665185, 3.637115993665185], [3.576085608246151, 3.313315766455653, 3.313315766455653, 3.313315766455653], [3.739600198542477, 3.5734180021212527, 4.034849342197791, 3.4671027317089025]]
MTSat
[[0.00129223798176, 0.0014841752890748, 0.0013368451408746, 0.0013368451408746], [0.0011388416775548, 0.001123306492997, 0.001036083901409, 0.0010984101977734], [0.0012773608831078, 0.0013156767241556, 0.0013540267986507, 0.0014153027257222], [0.0014153027257222, 0.0013227935588819, 0.0013498186815148, 0.0013498186815148], [0.0016271384699499, 0.0013811508940738, 0.0013811508940738, 0.0013811508940738], [0.0012395962831586, 0.0013018090136284, 0.0012232588411571, 0.0012559476536657]]
T1
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]
[[0.0010138856451204, 0.0010177543993774, 0.0010257196398529, 0.0010257196398529], [0.0014014718331852, 0.0009761721717434, 0.0009117604540341, 0.000815311519069], [0.0009605911746559, 0.0009906206359397, 0.0006694445137909, 0.0008935883019168], [0.0008935883019168, 0.0009645148099392, 0.0010351902433702, 0.0010351902433702], [0.0009774778167169, 0.0009774778167169, 0.0009774778167169, 0.0009774778167169], [0.0010551867192628, 0.001012210010244, 0.0010180580331023, 0.0009165329349018]]
[[0.0005942976466395, 0.0005960152894725, 0.00062691302888, 0.00062691302888], [0.0005112709262059, 0.0005704880839017, 0.0005137069084603, 0.0004143742226968], [0.0004672565333558, 0.0005026007210642, 0.0004066867643462, 0.0003393328073422], [0.0003393328073422, 0.0004692023931709, 0.0005123971557951, 0.0005123971557951], [0.0005045102052002, 0.0005045102052002, 0.0005045102052002, 0.0005045102052002], [0.000577999230138, 0.0005316527869437, 0.0005729917043376, 0.0004937373474434]]
[[44.209522055240505, 50.69960144846205, 45.682771475180594, 45.682771475180594], [42.67916913302598, 37.82261433907465, 44.258456219263856, 40.76688074907387], [47.497071935829645, 47.81068337186637, 47.57378502229639, 47.19708621549288], [47.19708621549288, 46.77334882206762, 47.79720317144616, 47.79720317144616], [46.802709566692286, 44.27238222794652, 44.27238222794652, 44.27238222794652], [47.15066198433709, 46.34750036374999, 48.02207246120396, 45.055435263858136]]
[[3.499265814909754, 3.80693641422522, 3.3575814030216278, 3.3575814030216278], [3.8557974910487354, 2.846363452702357, 4.075625383910599, 3.373417235607917], [3.7244854393057487, 3.704874827322425, 3.589619356583784, 3.442284461661099], [3.442284461661099, 3.539465912889603, 3.637115993665185, 3.637115993665185], [3.576085608246151, 3.313315766455653, 3.313315766455653, 3.313315766455653], [3.739600198542477, 3.5734180021212527, 4.034849342197791, 3.4671027317089025]]
[[0.00129223798176, 0.0014841752890748, 0.0013368451408746, 0.0013368451408746], [0.0011388416775548, 0.001123306492997, 0.001036083901409, 0.0010984101977734], [0.0012773608831078, 0.0013156767241556, 0.0013540267986507, 0.0014153027257222], [0.0014153027257222, 0.0013227935588819, 0.0013498186815148, 0.0013498186815148], [0.0016271384699499, 0.0013811508940738, 0.0013811508940738, 0.0013811508940738], [0.0012395962831586, 0.0013018090136284, 0.0012232588411571, 0.0012559476536657]]
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]
[[0.0010138856451204, 0.0010177543993774, 0.0010257196398529, 0.0010257196398529], [0.0014014718331852, 0.0009761721717434, 0.0009117604540341, 0.000815311519069], [0.0009605911746559, 0.0009906206359397, 0.0006694445137909, 0.0008935883019168], [0.0008935883019168, 0.0009645148099392, 0.0010351902433702, 0.0010351902433702], [0.0009774778167169, 0.0009774778167169, 0.0009774778167169, 0.0009774778167169], [0.0010551867192628, 0.001012210010244, 0.0010180580331023, 0.0009165329349018]]
[[0.0010138856451204, 0.0010177543993774, 0.0010257196398529, 0.0010257196398529], [0.0014014718331852, 0.0009761721717434, 0.0009117604540341, 0.000815311519069], [0.0009605911746559, 0.0009906206359397, 0.0006694445137909, 0.0008935883019168], [0.0008935883019168, 0.0009645148099392, 0.0010351902433702, 0.0010351902433702], [0.0009774778167169, 0.0009774778167169, 0.0009774778167169, 0.0009774778167169], [0.0010551867192628, 0.001012210010244, 0.0010180580331023, 0.0009165329349018]]
[[0.0005942976466395, 0.0005960152894725, 0.00062691302888, 0.00062691302888], [0.0005112709262059, 0.0005704880839017, 0.0005137069084603, 0.0004143742226968], [0.0004672565333558, 0.0005026007210642, 0.0004066867643462, 0.0003393328073422], [0.0003393328073422, 0.0004692023931709, 0.0005123971557951, 0.0005123971557951], [0.0005045102052002, 0.0005045102052002, 0.0005045102052002, 0.0005045102052002], [0.000577999230138, 0.0005316527869437, 0.0005729917043376, 0.0004937373474434]]
[[0.0005942976466395, 0.0005960152894725, 0.00062691302888, 0.00062691302888], [0.0005112709262059, 0.0005704880839017, 0.0005137069084603, 0.0004143742226968], [0.0004672565333558, 0.0005026007210642, 0.0004066867643462, 0.0003393328073422], [0.0003393328073422, 0.0004692023931709, 0.0005123971557951, 0.0005123971557951], [0.0005045102052002, 0.0005045102052002, 0.0005045102052002, 0.0005045102052002], [0.000577999230138, 0.0005316527869437, 0.0005729917043376, 0.0004937373474434]]
[[44.209522055240505, 50.69960144846205, 45.682771475180594, 45.682771475180594], [42.67916913302598, 37.82261433907465, 44.258456219263856, 40.76688074907387], [47.497071935829645, 47.81068337186637, 47.57378502229639, 47.19708621549288], [47.19708621549288, 46.77334882206762, 47.79720317144616, 47.79720317144616], [46.802709566692286, 44.27238222794652, 44.27238222794652, 44.27238222794652], [47.15066198433709, 46.34750036374999, 48.02207246120396, 45.055435263858136]]
[[44.209522055240505, 50.69960144846205, 45.682771475180594, 45.682771475180594], [42.67916913302598, 37.82261433907465, 44.258456219263856, 40.76688074907387], [47.497071935829645, 47.81068337186637, 47.57378502229639, 47.19708621549288], [47.19708621549288, 46.77334882206762, 47.79720317144616, 47.79720317144616], [46.802709566692286, 44.27238222794652, 44.27238222794652, 44.27238222794652], [47.15066198433709, 46.34750036374999, 48.02207246120396, 45.055435263858136]]
[[3.499265814909754, 3.80693641422522, 3.3575814030216278, 3.3575814030216278], [3.8557974910487354, 2.846363452702357, 4.075625383910599, 3.373417235607917], [3.7244854393057487, 3.704874827322425, 3.589619356583784, 3.442284461661099], [3.442284461661099, 3.539465912889603, 3.637115993665185, 3.637115993665185], [3.576085608246151, 3.313315766455653, 3.313315766455653, 3.313315766455653], [3.739600198542477, 3.5734180021212527, 4.034849342197791, 3.4671027317089025]]
[[3.499265814909754, 3.80693641422522, 3.3575814030216278, 3.3575814030216278], [3.8557974910487354, 2.846363452702357, 4.075625383910599, 3.373417235607917], [3.7244854393057487, 3.704874827322425, 3.589619356583784, 3.442284461661099], [3.442284461661099, 3.539465912889603, 3.637115993665185, 3.637115993665185], [3.576085608246151, 3.313315766455653, 3.313315766455653, 3.313315766455653], [3.739600198542477, 3.5734180021212527, 4.034849342197791, 3.4671027317089025]]
[[0.00129223798176, 0.0014841752890748, 0.0013368451408746, 0.0013368451408746], [0.0011388416775548, 0.001123306492997, 0.001036083901409, 0.0010984101977734], [0.0012773608831078, 0.0013156767241556, 0.0013540267986507, 0.0014153027257222], [0.0014153027257222, 0.0013227935588819, 0.0013498186815148, 0.0013498186815148], [0.0016271384699499, 0.0013811508940738, 0.0013811508940738, 0.0013811508940738], [0.0012395962831586, 0.0013018090136284, 0.0012232588411571, 0.0012559476536657]]
[[0.00129223798176, 0.0014841752890748, 0.0013368451408746, 0.0013368451408746], [0.0011388416775548, 0.001123306492997, 0.001036083901409, 0.0010984101977734], [0.0012773608831078, 0.0013156767241556, 0.0013540267986507, 0.0014153027257222], [0.0014153027257222, 0.0013227935588819, 0.0013498186815148, 0.0013498186815148], [0.0016271384699499, 0.0013811508940738, 0.0013811508940738, 0.0013811508940738], [0.0012395962831586, 0.0013018090136284, 0.0012232588411571, 0.0012559476536657]]
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]
[[0.6310385280039796, 0.6449939742310774, 0.6052019869249001, 0.6052019869249001], [0.799384499868077, 0.6294310187889507, 0.6595746693454234, 0.7172795640397259], [0.7262775593497328, 0.7112761015883302, 0.4787790887981428, 0.8113632640960852], [0.8113632640960852, 0.7323609952753036, 0.7224137607034387, 0.7224137607034387], [0.6983788722936425, 0.6983788722936425, 0.6983788722936425, 0.6983788722936425], [0.6649732448837092, 0.688663199247152, 0.6533355425960395, 0.6473157034113586]]